Browse by MODEL: No model

SASDNA6 – Ox40 RNA (untranslated region, UTR) constitutive decay element (CDEshort)

Ox40 3 UTR CDEshort experimental SAS data
Ox40 3 UTR CDEshort Kratky plot
Sample: Ox40 3 UTR CDEshort monomer, 5 kDa Mus musculus RNA
Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
Tants JN, Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 1.5 nm

SASDNB6 – Ox40 RNA (untranslated region, UTR) terminal stem (Terminusuucg)

Ox40 3 UTR Terminusuucg experimental SAS data
Ox40 3 UTR Terminusuucg Kratky plot
Sample: Ox40 3 UTR Terminusuucg monomer, 10 kDa Mus musculus RNA
Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 7
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
Tants JN, Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 1.6 nm
Dmax 5.5 nm
VolumePorod 16 nm3

SASDNC6 – Ox40 RNA (untranslated region, UTR), alternative decay element (ADEshort)

Ox40 3 UTR ADEshort experimental SAS data
Ox40 3 UTR ADEshort Kratky plot
Sample: Ox40 3 UTR ADEshort monomer, 7 kDa Mus musculus RNA
Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 7
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
Tants JN, Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 1.7 nm
Dmax 9.0 nm
VolumePorod 12 nm3

SASDM46 – c-Kit12 DNase I Digest

c-Kit 12-tract G-quadruplex monomer Dnase I treated experimental SAS data
c-Kit 12-tract G-quadruplex monomer Dnase I treated Kratky plot
Sample: C-Kit 12-tract G-quadruplex monomer Dnase I treated monomer, 20 kDa synthetic construct DNA
Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Sep 29
Long promoter sequences form higher-order G-quadruplexes: an integrative structural biology study of c-Myc, k-Ras and c-Kit promoter sequences. Nucleic Acids Res (2022)
Monsen RC, DeLeeuw LW, Dean WL, Gray RD, Chakravarthy S, Hopkins JB, Chaires JB, Trent JO
RgGuinier 1.6 nm
Dmax 5.7 nm
VolumePorod 16 nm3

SASDMM6 – cMyc-12

cMyc promoter 12-tract G-quadruplex experimental SAS data
cMyc promoter 12-tract G-quadruplex Kratky plot
Sample: CMyc promoter 12-tract G-quadruplex monomer, 23 kDa synthetic construct DNA
Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Mar 22
Long promoter sequences form higher-order G-quadruplexes: an integrative structural biology study of c-Myc, k-Ras and c-Kit promoter sequences. Nucleic Acids Res (2022)
Monsen RC, DeLeeuw LW, Dean WL, Gray RD, Chakravarthy S, Hopkins JB, Chaires JB, Trent JO
RgGuinier 2.3 nm
Dmax 8.4 nm
VolumePorod 29 nm3

SASDK52 – TAF1 tandem bromodomain

Transcription initiation factor II D experimental SAS data
Transcription initiation factor II D Kratky plot
Sample: Transcription initiation factor II D monomer, 31 kDa Escherichia coli protein
Buffer: 50 mM HEPES, 5% v/v ethylene glycol, 2.5% v/v DMSO and 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2019 Oct 26
Discovery of Dual TAF1-ATR Inhibitors and Ligand-Induced Structural Changes of the TAF1 Tandem Bromodomain. J Med Chem 65(5):4182-4200 (2022)
Karim RM, Yang L, Chen L, Bikowitz MJ, Lu J, Grassie D, Shultz ZP, Lopchuk JM, Chen J, Schönbrunn E
RgGuinier 2.6 nm
Dmax 7.3 nm
VolumePorod 50 nm3

SASDK62 – TAF1 tandem bromodomain with inhibitor AZD6738

Transcription initiation factor II D experimental SAS data
Transcription initiation factor II D Kratky plot
Sample: Transcription initiation factor II D monomer, 31 kDa Escherichia coli protein
Buffer: 50 mM HEPES, 5% v/v ethylene glycol, 2.5% v/v DMSO and 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2019 Oct 19
Discovery of Dual TAF1-ATR Inhibitors and Ligand-Induced Structural Changes of the TAF1 Tandem Bromodomain. J Med Chem 65(5):4182-4200 (2022)
Karim RM, Yang L, Chen L, Bikowitz MJ, Lu J, Grassie D, Shultz ZP, Lopchuk JM, Chen J, Schönbrunn E
RgGuinier 2.3 nm
Dmax 6.6 nm
VolumePorod 44 nm3

SASDK72 – TAF1 tandem bromodomain with inhibitor BAY299

Transcription initiation factor II D experimental SAS data
Transcription initiation factor II D Kratky plot
Sample: Transcription initiation factor II D monomer, 31 kDa Escherichia coli protein
Buffer: 50 mM HEPES, 5% v/v ethylene glycol, 2.5% v/v DMSO and 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2019 Oct 19
Discovery of Dual TAF1-ATR Inhibitors and Ligand-Induced Structural Changes of the TAF1 Tandem Bromodomain. J Med Chem 65(5):4182-4200 (2022)
Karim RM, Yang L, Chen L, Bikowitz MJ, Lu J, Grassie D, Shultz ZP, Lopchuk JM, Chen J, Schönbrunn E
RgGuinier 3.6 nm
Dmax 12.5 nm
VolumePorod 106 nm3

SASDKJ8 – CUB domain-containing protein 1 (CDCP1)

CUB domain-containing protein 1 experimental SAS data
CUB domain-containing protein 1 Kratky plot
Sample: CUB domain-containing protein 1 monomer, 77 kDa Homo sapiens protein
Buffer: 10 mM phosphate, 137 mM NaCl, 2.7 mM KCl,, pH: 7.4
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2020 Jul 29
Targeting a proteolytic neoepitope on CUB domain containing protein 1 (CDCP1) for RAS-driven cancers. J Clin Invest 132(4) (2022)
Lim SA, Zhou J, Martinko AJ, Wang YH, Filippova EV, Steri V, Wang D, Remesh SG, Liu J, Hann B, Kossiakoff AA, Evans MJ, Leung KK, Wells JA
RgGuinier 4.4 nm
Dmax 14.5 nm
VolumePorod 185 nm3

SASDKK8 – Cleaved CUB domain containing protein 1 (CDCP1)

Cleaved - CUB domain-containing protein 1 (N-terminus)Cleaved - CUB domain-containing protein 1 (C-terminus) experimental SAS data
Cleaved - CUB domain-containing protein 1 (N-terminus) Cleaved - CUB domain-containing protein 1 (C-terminus) Kratky plot
Sample: Cleaved - CUB domain-containing protein 1 (N-terminus) monomer, 38 kDa Homo sapiens protein
Cleaved - CUB domain-containing protein 1 (C-terminus) monomer, 39 kDa Homo sapiens protein
Buffer: 10 mM phosphate, 137 mM NaCl, 2.7 mM KCl,, pH: 7.4
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2020 Jul 29
Targeting a proteolytic neoepitope on CUB domain containing protein 1 (CDCP1) for RAS-driven cancers. J Clin Invest 132(4) (2022)
Lim SA, Zhou J, Martinko AJ, Wang YH, Filippova EV, Steri V, Wang D, Remesh SG, Liu J, Hann B, Kossiakoff AA, Evans MJ, Leung KK, Wells JA
RgGuinier 4.4 nm
Dmax 14.3 nm
VolumePorod 182 nm3